Rivers are the primary contributors of iron and other elements to the global oceans. Iron-reducing bacteria play an important biogeochemical role in coupling the iron and carbon redox cycles. However, the extent of changes in community structures and iron-reduction activities of iron-reducing bacteria in riverine and coastal marine sediments remains unclear. This study presents information on the spatial patterns and relative abundance of iron-reducing bacteria in sediments of the Yellow River estuary and the adjacent Bohai Sea. High-throughput sequencing of bacterial 16S rRNA found that the highest relative abundances and diversities were from the estuary (Yellow River–Bohai Sea mixing zone). Pseudomonas, Thiobacillus, Geobacter, Rhodoferax, and Clostridium were the most abundant putative iron-reducing bacteria genera in the sediments of the Yellow River. Vibrio, Shewanella, and Thiobacillus were the most abundant in the sediments of the Bohai Sea. The putative iron-reducing bacterial community was positively correlated with the concentrations of total nitrogen and ammonium in coastal marine sediments, and was significantly correlated with the concentration of nitrate in river sediments. The riverine sediments, with a more diverse iron-reducing bacterial community, exhibited increased activity of Fe(III) reduction in enrichment cultures. The estuary-wide high abundance of putative iron-reducing bacteria suggests that the effect of river–sea interaction on bacterial distribution patterns is high. The results of this study will help the understanding of the biogeochemical cycling of iron in riverine and coastal marine environments.